5WRC | pdb_00005wrc

Crystal structure of proteinase K from Engyodontium album

• PDB DOI: https://doi.org/10.2210/pdb5WRC/pdb

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Expression System: Parengyodontium album
• Mutation(s): No 


• Deposited: 2016-12-01 Released: 2017-11-29 
• Deposition Author(s): Sugahara, M., Nakane, T., Suzuki, M., Masuda, T., Inoue, S., Numata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Hydroxyethyl cellulose matrix applied to serial crystallography

Sugahara, M., Nakane, T., Masuda, T., Suzuki, M., Inoue, S., Song, C., Tanaka, R., Nakatsu, T., Mizohata, E., Yumoto, F., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Nureki, O., Numata, K., Nango, E., Iwata, S.

(2017) Sci Rep 7: 703-703

• PubMed: 28386083 
• DOI: https://doi.org/10.1038/s41598-017-00761-0
• Primary Citation Related Structures: 
  5WR8, 5WR9, 5WRA, 5WRB, 5WRC


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Department of Physics, POSTECH, Pohang, 37673, Republic of Korea.
Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Structural Biology Research Center, KEK High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama, 351-0198, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.3 kDa 
• Atom Count: 2,252 
• Modeled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0  Gene Names: PROK EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR	C [auth A], D [auth A]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1350030

Diffraction Data: https://doi.org/10.11577/1350028

Diffraction Data: https://doi.org/10.11577/1350031

Diffraction Data: https://doi.org/10.11577/1350029

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.6	α = 90
b = 68.6	β = 90
c = 108.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data processing
CrystFEL	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Sugahara, M., Nakane, T., Suzuki, M., Masuda, T., Inoue, S., Numata, K.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Data collection
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-11-13
  Changes: Structure summary